Molecular and Cellular Neuroscience Commons^™

Flash4 Dark Reference Images, George Mcnamara

George McNamara

Hamamatsu FLASH4.0 dark reference images, acquired with 10 second exposure times, no light to camera. Camera offset (set by Hamamatsu( is ~100 (the average intensity of the first image is always ~1 intensity level higher - an odd feature, but trivial in practice for a 16-bit camera).

George McNamara, Ph.D.

Single Cells Analyst at L.J.N. Cooper Lab

University of Texas M.D. Anderson Cancer Center

Video Codec Performance (Excel Spreadsheet), George Mcnamara

George McNamara

Video codec performance (Excel spreadsheet). Movie was made in 2005-2006 when I worked at City of Hope National Medical Center. VTLF refers to Video Timelapse Light Facility. Videos were outputted from MetaMorph as AVI files. Personally, I always recommend uncompressed video files fro scientific uses. I also encourage posting the original scientific data format (ex. .lsm, .zvi, .lif, .stk).

Pubspectra Tattletales, George Mcnamara

George McNamara

Tattletales for Multiplex Fluorescent Reporters in Single Cells for Metabolomics

George McNamara

As of April 2013: L.J.N. Cooper & D.A. Lee Cellular Immunotherapy Lab, University of Texas M.D. Anderson Cancer Center, Houston, TX

Email: gtmcnamara@mdanderson.org, geomcnamara@earthlink.net

Tattletales is my concept for spatial multiplexing many fluorescent protein (FP) biosensors in the same live cell. For example, there are excellent FP biosensors to Ca++ ions, pH, glucose, ribose, glutamine, glutamate, ATP, redox, ROS, pyruvate, cAMP, cGMP, IP3, PI(3,4,5)P3, cell cycle indicators (Fucci2), PKA, PKC, photsphatases, caspase(s) [1, 2]. However, these are typically used one biosensor per experiment, due in part to flooding …

Application Of Three-Dimensional Culture Conditions To Human Embryonic Stem Cell-Derived Definitive Endoderm Cells Enhances Hepatocyte Differentiation And Functionality, Thamil Selvee Ramasamy

Thamil Selvee Ramasamy

Human embryonic stemcells (hESCs) and induced pluripotent stemcells (iPSCs) provide an unlimited source for the generation of human hepatocytes, owing to their indefinite self-renewal and pluripotent properties. Both hESC-/iPSC-derived hepatocytes hold great promise in treating liver diseases as potential candidates for cell replacement therapies or as an in vitro platform to conduct newdrug trials. It has been previously demonstrated that the initiation of hESC differentiation in monolayer cultures increases the generation of definitive endoderm (DE) and subsequently of hepatocyte differentiation. However, monolayer culture may hinder the maturation of hESC-derived hepatocytes, since such two-dimensional (2D) conditions do not accurately reflect the …

Halloween 2012 Jack O'Lanterns Trick Or Treat, George Mcnamara

George McNamara

Halloween 2012 makes trick or treating more visual and interactive than in past years.

the download is a ZIP file containing three files.

Print out the (unnumbered) image on as large and nice printer paper as possible - I used glossy 44" wide here in Miami (University of Miami, MillerSchool of Medicine, Calder Library, Biomedical Communications dept - I also made another print on "fabric", also 44" wide to take with me to an HHMI Janelia Farm conference on 'turning images into knowledge' that ends on Oct 31 - might stay up for a second conference, "GFP..." that start Nov …

Mcnamara 20120831fri-20120904tue Cosmic Ray Particles By Ccd Imaging, George Mcnamara

George McNamara

McNamara 20120831Fri-20120904Tue Cosmic Ray Particles by CCD imaging.zip contains image files in support of a Microscopy Today article - please see

http://www.microscopy-today.com/

Cosmic Ray Particles Images With Orca-Ii Erg, George Mcnamara

George McNamara

Cosmic ray particles image series acquired using a Hamamatsu ORCA-II ERG scientific grade CCD camera, cooled to -60 C. Each image is a consecutive 600 second (10 minute) exposure time with no light to the camera.

While processing the data, I discoverd that the background changed around planes 25 and 227 (see Excel file and jpeg screenshots), so I also processed only planes 025-227 (203 planes total, 2030 minutes, 33.83 hours). the CCD industry "rule of thumb" for a "typical" CCD sensor (i.e. 1/3" CCD) is that one cosmic ray particle strikes a sensor approximately every 30 seconds (assuming not …

Flatbed Scanner Report - Optical Density Dynamic Range, George Mcnamara

George McNamara

George McNamara (now at University of Miami) report for Hua Yu and Richard Jove, City of Hope National Medical Center, on optical density dynamic range of several flatbed scanners.

Introduction To Nanoscopy Nano-Talk, George Mcnamara

George McNamara

T7-1 is the designation for the LMRG Nanoscopy session at ABRF in Orlando, FL, on March 20, 2012. The PDF file here is a draft of my presentation.

May not be very helpful since (1) would probably help to know what is in my head and each slide will [hopefully] prompt me to say, and (2) 10 minute talk so I am going to push the "next slide" button after saying very little.

__________________

Publisher statement:

The T7-1 Introduction to Nanoscopy Nano Talk is copyrighted (c) George McNamara, 2012. Except for (1) screenshots from research articles (which are copyrighted by …

Pubspectra - Open Data Access Fluorescence Spectra, George Mcnamara

George McNamara

The Internet is enabling greater access to spectral imaging publications, spectral graphs, and data than that was available a generation ago. The spectral imaging systems discussed in this issue of Cytometry work because reagent and hardware spectra are reproducible, reusable, and provide input to spectral unmixing and spectral components recognition algorithms. These spectra need to be readily available in order to determine what to purchase, how to use it, and what the output means. We refer to several commercially sponsored and academic spectral web sites and discuss our spectral graphing and data sites. Sites include fluorescent dye graph servers from …

Mcnamara 2011 Feature Extraction (Image Analysis), George Mcnamara

George McNamara

Feature Extraction presentation and movies in a ZIP file from a presentation I gave at ISAC 2011 in Baltomore, Md.

Feature extraction is one phrase for image analysis.

Rogers Pmn Movie - Background Information, George Mcnamara

George McNamara

Please see

http://mdc.custhelp.com/app/answers/detail/a_id/18689/~/metamatters-newsletters

for my series of MetaMorph MetaMatters articles in volume 2, numbers 3 through 6, on the Rogers PMN Panorama data set.

http://mdc.custhelp.com/app/answers/detail/a_id/18689/~/metamatters-newsletters

Brief summary (for more, see the Word doc)

Mcnamara 2011 Mpmicro - Multi-Probe Microscopy (10/31/2011), George Mcnamara

George McNamara

Multi-Probe Microscopy is an ~1500 page Word document summarizing what I know and/or found interesting in light microscopy, fluorescence microscopy and digital image analysis, from 1995-2005. Very little has been updated since 2005.

Lack Of Depolarization-Induced Suppression Of Inhibition (Dsi) In Layer 2/3 Interneurons That Receive Cannabinoid-Sensitive Inhibitory Inputs, Fouad Lemtiri-Chlieh, Eric S. Levine

fouad Lemtiri-Chlieh

In layer 2/3 of neocortex, brief trains of action potentials in pyramidal neurons (PNs) induce the mobilization of endogenous cannabinoids (eCBs), resulting in a depression of GABA release from the terminals of inhibitory interneurons (INs). This depolarization-induced suppression of inhibition (DSI) is mediated by activation of the type 1 cannabinoid receptor (CB1) on presynaptic terminals of a subset of INs. However, it is not clear whether CB1 receptors are also expressed at synapses between INs, and whether INs can release eCBs in response to depolarization. In the present studies, brain slices containing somatosensory cortex were prepared from 14- to 21-day-old …

Inhibition Of Astroglial Kir4.1 Channels By Selective Serotonin Reuptake Inhibitors, Y. Ohno, H. Hibino, Christoph Lossin, A. Inanobe, Y. Kurachi

Christoph Lossin, Ph.D.

The inwardly rectifying K+ (Kir) channel Kir4.1 is responsible for astroglial K+ buffering. We recently found that tricyclic antidepressants (TCAs) inhibit Kir4.1 channel currents, which suggests that astroglial Kir currents might be involved in the pharmacological action of antidepressants. We therefore further examined the effects of the currently most popular antidepressants, selective serotonin reuptake inhibitors (SSRIs), and other related agents on Kir4.1 channels heterologously expressed in HEK293T cells. The whole-cell patch clamp technique was used. Fluoxetine, the typical SSRI, inhibited Kir4.1 channel currents in a concentration-dependent manner with an IC50 value of 15.2 microM. The inhibitory effect of fluoxetine was …

Inhibition Of Astroglial Inwardly Rectifying Kir4.1 Channels By A Tricyclic Antidepressant, Nortriptyline., S. Su, Y. Ohno, Christoph Lossin, A. Inanobe, Y. Kurachi

Christoph Lossin, Ph.D.

The inwardly rectifying K(+) (Kir) channel Kir4.1 is responsible for astroglial K(+) buffering. We examined the effects of nortriptyline, a tricyclic antidepressant (TCA), on Kir4.1 channel currents heterologously expressed in HEK293T cells, using a whole-cell patch-clamp technique. Nortriptyline (3-300 microM) reversibly inhibited Kir4.1 currents in a concentration-dependent manner, whereas it marginally affected neuronal Kir2.1 currents. The inhibition of Kir4.1 channels by nortriptyline depended on the voltage difference from the K(+) equilibrium potential (E(K)), with greater potency at more positive potentials. Blocking kinetics of the drug could be described by first-order kinetics, where dissociation of the drug slowed down and association …

Non-Inactivating Voltage-Gated Sodium Channels In Severe Myoclonic Epilepsy Of Infancy, T. H. Rhodes, Christoph Lossin, C. Vanoye, Alfred L. George

Christoph Lossin, Ph.D.

Mutations in SCN1A, the gene encoding the brain voltage-gated sodium channel alpha(1) subunit (Na(V)1.1), are associated with at least two forms of epilepsy, generalized epilepsy with febrile seizures plus and severe myoclonic epilepsy of infancy (SMEI). We examined the functional properties of five SMEI mutations by using whole-cell patch-clamp analysis of heterologously expressed recombinant human SCN1A. Two mutations (F902C and G1674R) rendered SCN1A channels nonfunctional, and a third allele (G1749E) exhibited minimal functional alterations. However, two mutations within or near the S4 segment of the fourth repeat domain (R1648C and F1661S) conferred significant impairments in fast inactivation, including persistent, noninactivating …

Intrinsic Role Of Polysialylated Neural Cell Adhesion Molecule In Photic Phase Resetting Of The Mammalian Circadian Clock, Rebecca Prosser

Rebecca Prosser

The suprachiasmatic nuclei (SCN), the location of the mammalian circadian clock, are one of the few adult brain regions that express the highly polysialylated form of neural cell adhesion molecule (PSA-NCAM). A role for the polysialic acid (PSA) component of PSA-NCAM, which is known to promote tissue plasticity, has been reported for photic entrainment of circadian rhythmicity in vivo. The in vivo results, however, do not discriminate between PSA acting upstream or downstream of the glutamatergic synapses that convey photic information to the SCN. To address this key issue, we exploited an in vitro rat brain slice preparation that retains …

Presence Of A Cs-Resistant Transient Outward Current Which Distorts Ica Measurements In Guinea-Pig Single Ventricular Cells, Georges Christé, Brigitte Delachapelle, Fouad Lemtiri-Chlieh, Carlos Ojeda

fouad Lemtiri-Chlieh

To correctlyr analyse the physical properties of ion channels and the actions of drugs upon them, it is important that the membrane conducts only the ionic species believed permeant. In guinea-pig ventricular cells it has been assumed that only ICaL flows in the potential range -50 to +60 mV in the presence of intra- and extracellular Cs (> 20 mM). We report here that this is not the case due to the presence of a Cs-insensitive, transient outward current.

Measurements Of Cytosolic Free Ca In Cultured Rat Neonate And Adult Guinea-Pig Ventricular Cardiac Myocytes, Jean-Claude Bernengo, Fouad Lemtiri-Chlieh, Carlos Ojeda, Nadine Pltonoff

fouad Lemtiri-Chlieh

Cytosolic free Ca was measured with Indo-1 (Grynkiewicz et al. 1985) as free acid (in guinea-pig cells) or as the ester (in rat neonate cells). Using image analysis we obtained concentration maps at 40 ms intervals at two wavelengths (Cannell et al. 1986). In rat neonate cells, at rest and during contraction, calcium was apparently non-uniformly distributed, in contrast to guinea-pig adult cells. Using a dual PM spectroscopic system adapted to an inverted microscope we found: (1) the conversion of Indo-AM to Indo- 1 in the cytosol is not complete (< 40% contribution to the total light); (2) rat neonate cells buffer Ca (at rest 130-170 nM) only for [Ca]. between 1 and 3 mM, whereas in adult guinea-pig cells the range extended to 10 mM; (3) during contraction [Ca]i rose from 200 nm to no more than 1 microM. Digitoxin increases basal and peak [Ca]i; (4) during spontaneous contractions, in guinea-pig cells, [Ca]i rises from 70 to 200 nm when [Ca]o = 0, and from 170 nm to about 1 microM when [Ca]o = 2 mM; (5) in voltage-clamp conditions the rise in [Ca]i does not exceed 2 microM and oscillations occur in the presence of forskolin. When loading with Indo-1, cells frequently cease to contract (Powell et al. 1988) and the variations in [Ca]i are then very small (about 200 nm at peak ICa). In both cases these values are small compared to the total charge crossing the membrane.